In order to analyze the molecular epidemiology of A (H1N1) influenza virus in 2009, the complete genome sequences of influenza strains from different host sources downloaded from the NCBI were analyzed on genetic evolution by DNAstar software in this research. The results showed that 79 mutation sites of new A (H1N1) influenza virus were observed compared to previous human A (H1N1) influenza strain, including 14 mutation sites new in all A (H1N1) influenza sources and 37 mutation sites only observed in swine strain. A significant difference was represented in antigenic sites between new A (H1N1) influenza strain and the previous human A (H1N1) strain. This phenomenon shows the new A (H1N1) influenza strain is either originated from the recombination of human and swine strain or from the infection in pig populations and gradual mutation to human tansmission, which remains to be further studied.